Before Abyssea I checked things like Vrtra and Jormungand specifically because they weren't as heavily camped, and I was thinking about starting a shell to do them for the cash drops. They were actually pretty rare to come across. The big HNM shells on my server didn't let them roam very long unless something bigger was due to pop.
Even though the only NM I fought was Charybdis I have to admit it was fun. Only thing that topped it was Sky. I can only imagine what it was like to drop the ground kings, in a way I feel I missed out. Not that I missed out on the loot, but the experience of taking them out.
And instances really are no different on the work = reward front. I saw people camp things for months on end in FFXI to never see it. Conversly in WoW, which generally hands out gear like a pez dispenser, I watched a buddy of mine run an instance hundreds of times and never once see the item he was after. Matter of fact, he'd been running it a month solid when I caught up to him and started running the same one since it held 2 pieces I needed. I got my 2 pieces of gear, and to this day we still haven't seen his drop. I've even solo'd it for fun once they raised the cap, no dice. For reference, it was something he needed in BC to tank as Paladin. I wanna say a shield? And he couldn't get into higher tiers than Heroics because of lack of this item. Pretty well locked him out of BC raiding on that toon, because pally healing is boring as hell and back then Ret Paladin was the lolDRG of WoW.
I've also seen gear ninja looted during instances. I've seen PuG raid leaders show blatant favoritism and slip a guildmate an item without giving everyone a fair chance to roll on it. In a way I couldn't complain, it was a best friend IRL slipping me (the only hunter) a bow, but that's besides the point. IIRC it did cause one of our PuG'd members to drop group, and I couldn't blame him.
Everything has it's drawbacks. Even BCNM/KSNM. I don't even remember how many times I ran BCNM/KSNMs that people could typically net 1M in gil from, and only gotten around 15k. I'm sure there's someone out there that did the BCNM (or was it KSNM?) of Faffhog countless times and never saw anything worth a damn from it.
Edit: Forgot the point of all that, which isn't just ranting. Point was, the fact that drawbacks exist doesn't mean the content shouldn't. Just that you as a player need to decide which content is right for you and do that. We shouldn't be like WoW and narrow our PVE content down to Heroics and Raids or Heroics and Raids - now with "hard" mode! Diversity is a good thing.